0.016964
-0.000000
-0.000000
0.000000
0.011686
-0.000000
0.000000
0.000000
0.021510
0.000000
0.000000
0.000000
Stout, C.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.000
90.000
90.000
58.950
85.570
46.490
C50 H64 N6 O10
909.077
benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate
TL-3, C2 symmetric inhibitor
peptide-like
C7 H14 O
114.185
(1S,2S)-2-methylcyclohexanol
trans-2-methylcyclohexanol
non-polymer
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C2 H6 O S
78.133
BETA-MERCAPTOETHANOL
non-polymer
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C2 H6 O S
78.133
DIMETHYL SULFOXIDE
non-polymer
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
K 1
39.098
POTASSIUM ION
non-polymer
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
C
N
2
N
O
N
3
N
O
N
4
N
C
Y
5
N
C
Y
6
N
C
Y
7
N
C
Y
8
N
C
Y
9
N
C
Y
10
N
C
N
11
N
N
N
12
S
C
N
13
N
C
N
14
N
O
N
15
N
C
N
16
N
N
N
17
S
C
N
18
N
C
N
19
N
O
N
20
N
C
N
21
N
C
N
22
N
C
N
23
R
C
N
24
N
O
N
25
S
C
N
26
N
N
N
27
N
C
Y
28
N
C
Y
29
N
C
Y
30
N
C
Y
31
N
C
Y
32
N
C
Y
33
N
C
N
34
N
N
N
35
S
C
N
36
R
C
N
37
N
O
N
38
N
C
Y
39
N
C
Y
40
N
C
Y
41
N
C
Y
42
N
C
Y
43
N
C
Y
44
N
C
N
45
N
N
N
46
S
C
N
47
N
C
N
48
N
O
N
49
N
C
N
50
N
C
N
51
N
C
N
52
N
N
N
53
S
C
N
54
N
C
N
55
N
O
N
56
N
C
N
57
N
C
N
58
N
O
N
59
N
O
N
60
N
C
Y
61
N
C
Y
62
N
C
Y
63
N
C
Y
64
N
C
Y
65
N
C
Y
66
N
C
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
C
N
132
S
C
N
133
N
C
N
134
N
C
N
135
N
C
N
136
N
C
N
137
S
C
N
138
N
O
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
N
N
154
S
C
N
155
N
C
N
156
N
O
N
157
N
C
N
158
N
O
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
N
N
167
S
C
N
168
N
C
N
169
N
O
N
170
N
C
N
171
N
C
N
172
N
C
N
173
N
N
N
174
N
C
N
175
N
N
N
176
N
N
N
177
N
O
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
N
N
194
S
C
N
195
N
C
N
196
N
O
N
197
N
C
N
198
N
C
N
199
N
O
N
200
N
N
N
201
N
O
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
N
N
211
S
C
N
212
N
C
N
213
N
O
N
214
N
C
N
215
N
C
N
216
N
O
N
217
N
O
N
218
N
O
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
C
N
227
N
C
N
228
N
O
N
229
N
S
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
N
N
237
R
C
N
238
N
C
N
239
N
O
N
240
N
C
N
241
N
S
N
242
N
O
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
S
N
251
N
O
N
252
N
C
N
253
N
C
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
N
N
261
S
C
N
262
N
C
N
263
N
O
N
264
N
C
N
265
N
C
N
266
N
C
N
267
N
O
N
268
N
N
N
269
N
O
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
N
N
281
S
C
N
282
N
C
N
283
N
O
N
284
N
C
N
285
N
C
N
286
N
C
N
287
N
O
N
288
N
O
N
289
N
O
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
N
N
300
N
C
N
301
N
C
N
302
N
O
N
303
N
O
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
N
N
310
S
C
N
311
N
C
N
312
N
O
N
313
N
C
Y
314
N
C
Y
315
N
N
Y
316
N
C
Y
317
N
C
Y
318
N
N
N
319
N
O
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
O
N
331
N
H
N
332
N
H
N
333
N
N
N
334
S
C
N
335
N
C
N
336
N
O
N
337
S
C
N
338
N
C
N
339
N
C
N
340
N
C
N
341
N
O
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
K
N
356
N
N
N
357
S
C
N
358
N
C
N
359
N
O
N
360
N
C
N
361
N
C
N
362
N
C
N
363
N
C
N
364
N
O
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
N
N
379
S
C
N
380
N
C
N
381
N
O
N
382
N
C
N
383
N
C
N
384
N
C
N
385
N
C
N
386
N
N
N
387
N
O
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
N
N
404
S
C
N
405
N
C
N
406
N
O
N
407
N
C
N
408
N
C
N
409
N
S
N
410
N
C
N
411
N
O
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
H
N
423
N
N
N
424
S
C
N
425
N
C
N
426
N
O
N
427
N
C
Y
428
N
C
Y
429
N
C
Y
430
N
C
Y
431
N
C
Y
432
N
C
Y
433
N
C
N
434
N
O
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
N
N
447
S
C
N
448
N
C
N
449
N
O
N
450
N
C
N
451
N
C
N
452
N
C
N
453
N
O
N
454
N
H
N
455
N
H
N
456
N
H
N
457
N
H
N
458
N
H
N
459
N
H
N
460
N
H
N
461
N
H
N
462
N
H
N
463
N
N
N
464
S
C
N
465
N
C
N
466
N
O
N
467
R
C
N
468
N
O
N
469
N
C
N
470
N
O
N
471
N
H
N
472
N
H
N
473
N
H
N
474
N
H
N
475
N
H
N
476
N
H
N
477
N
H
N
478
N
H
N
479
N
H
N
480
N
N
N
481
S
C
N
482
N
C
N
483
N
O
N
484
N
C
Y
485
N
C
Y
486
N
C
Y
487
N
C
Y
488
N
N
Y
489
N
C
Y
490
N
C
Y
491
N
C
Y
492
N
C
Y
493
N
C
N
494
N
O
N
495
N
H
N
496
N
H
N
497
N
H
N
498
N
H
N
499
N
H
N
500
N
H
N
501
N
H
N
502
N
H
N
503
N
H
N
504
N
H
N
505
N
H
N
506
N
H
N
507
N
N
N
508
S
C
N
509
N
C
N
510
N
O
N
511
N
C
Y
512
N
C
Y
513
N
C
Y
514
N
C
Y
515
N
C
Y
516
N
C
Y
517
N
C
N
518
N
O
N
519
N
O
N
520
N
H
N
521
N
H
N
522
N
H
N
523
N
H
N
524
N
H
N
525
N
H
N
526
N
H
N
527
N
H
N
528
N
H
N
529
N
H
N
530
N
H
N
531
N
N
N
532
S
C
N
533
N
C
N
534
N
O
N
535
N
C
N
536
N
C
N
537
N
C
N
538
N
O
N
539
N
H
N
540
N
H
N
541
N
H
N
542
N
H
N
543
N
H
N
544
N
H
N
545
N
H
N
546
N
H
N
547
N
H
N
548
N
H
N
549
N
H
N
1
N
doub
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
Y
8
N
doub
Y
9
N
sing
Y
10
N
sing
N
11
N
sing
Y
12
N
doub
N
13
N
sing
Y
14
N
sing
N
15
N
sing
Y
16
N
doub
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
doub
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
doub
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
Y
57
N
doub
Y
58
N
sing
Y
59
N
sing
N
60
N
sing
Y
61
N
doub
N
62
N
sing
Y
63
N
doub
N
64
N
sing
Y
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
Y
80
N
doub
Y
81
N
sing
Y
82
N
sing
N
83
N
sing
Y
84
N
doub
N
85
N
sing
Y
86
N
doub
N
87
N
sing
Y
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
doub
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
doub
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
doub
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
Y
123
N
doub
Y
124
N
sing
Y
125
N
sing
N
126
N
sing
Y
127
N
doub
N
128
N
sing
Y
129
N
sing
N
130
N
sing
Y
131
N
doub
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
doub
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
doub
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
doub
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
doub
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
doub
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
doub
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
doub
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
doub
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
doub
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
doub
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
doub
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
doub
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
doub
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
doub
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
doub
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
Y
313
N
sing
Y
314
N
doub
Y
315
N
doub
N
316
N
sing
Y
317
N
sing
N
318
N
sing
Y
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
doub
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
doub
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
doub
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
doub
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
sing
N
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
doub
N
417
N
sing
N
418
N
sing
N
419
N
sing
N
420
N
sing
Y
421
N
doub
Y
422
N
sing
Y
423
N
sing
N
424
N
sing
Y
425
N
doub
N
426
N
sing
Y
427
N
doub
N
428
N
sing
Y
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
sing
N
435
N
sing
N
436
N
sing
N
437
N
sing
N
438
N
sing
N
439
N
doub
N
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
sing
N
450
N
sing
N
451
N
sing
N
452
N
sing
N
453
N
sing
N
454
N
sing
N
455
N
sing
N
456
N
doub
N
457
N
sing
N
458
N
sing
N
459
N
sing
N
460
N
sing
N
461
N
sing
N
462
N
sing
N
463
N
sing
N
464
N
sing
N
465
N
sing
N
466
N
sing
N
467
N
sing
N
468
N
sing
N
469
N
sing
N
470
N
sing
N
471
N
sing
N
472
N
doub
N
473
N
sing
N
474
N
sing
N
475
N
sing
N
476
N
sing
Y
477
N
doub
Y
478
N
sing
Y
479
N
sing
N
480
N
sing
Y
481
N
doub
Y
482
N
sing
Y
483
N
sing
N
484
N
sing
Y
485
N
sing
Y
486
N
doub
N
487
N
sing
Y
488
N
doub
N
489
N
sing
Y
490
N
sing
N
491
N
sing
N
492
N
sing
N
493
N
sing
N
494
N
sing
N
495
N
sing
N
496
N
sing
N
497
N
sing
N
498
N
sing
N
499
N
sing
N
500
N
doub
N
501
N
sing
N
502
N
sing
N
503
N
sing
N
504
N
sing
Y
505
N
doub
Y
506
N
sing
Y
507
N
sing
N
508
N
sing
Y
509
N
doub
N
510
N
sing
Y
511
N
doub
N
512
N
sing
Y
513
N
sing
N
514
N
sing
N
515
N
sing
N
516
N
sing
N
517
N
sing
N
518
N
sing
N
519
N
sing
N
520
N
sing
N
521
N
sing
N
522
N
sing
N
523
N
sing
N
524
N
doub
N
525
N
sing
N
526
N
sing
N
527
N
sing
N
528
N
sing
N
529
N
sing
N
530
N
sing
N
531
N
sing
N
532
N
sing
N
533
N
sing
N
534
N
sing
N
535
N
sing
US
Chem.Biol.Drug Des.
1747-0277
75
257
268
10.1111/j.1747-0285.2009.00943.x
20659109
Fragment-based screen against HIV protease.
2010
10.2210/pdb3kfn/pdb
pdb_00003kfn
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
100
1
Rh coated flat mirror
CCD
2009-04-17
ADSC QUANTUM 315r
Side scattering I-beam bent single crystal, asymmetric cut 4.9650 deg.
SINGLE WAVELENGTH
M
x-ray
1
0.97946
1.0
BL7-1
SSRL
0.97946
SYNCHROTRON
SSRL BEAMLINE BL7-1
10831.833
Protease
3.4.23.16
2
man
polymer
909.077
benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate
1
syn
non-polymer
114.185
(1S,2S)-2-methylcyclohexanol
1
syn
non-polymer
78.133
DIMETHYL SULFOXIDE
4
syn
non-polymer
39.098
POTASSIUM ION
2
syn
non-polymer
78.133
BETA-MERCAPTOETHANOL
1
syn
non-polymer
18.015
water
201
nat
water
no
no
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
A,B
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
R8
sample
POL
11676
Human immunodeficiency virus 1
562
Escherichia coli
BL21.DE3
PLASMID
PET 21A+
1
2.71
54.55
VAPOR DIFFUSION
7.0
0.5 M KSCN, 0.1 M MES-HCL, pH 7.0, 10% DMSO, VAPOR DIFFUSION, temperature 277K
277
database_2
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
repository
Initial release
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Version format compliance
Other
Database references
Derived calculations
Data collection
Refinement description
1
0
2010-02-23
1
1
2011-07-13
1
2
2013-02-27
1
3
2021-10-13
1
4
2023-09-06
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
HIV-1 PROTEASE NL4-3 IN COMPLEX WITH INHIBITOR, TL-3, WILD TYPE
HIV Protease with fragment 4D9 bound
HIV Protease (PR) dimer without inhibitor; acetate in exo site
HIV Protease (PR) with inhibitor TL-3 bound, and DMSOs in exo site
HIV Protease (PR) dimer with inhibitor TL-3 bound and fragment 1F1 in the outside/top of flap
HIV Protease (PR) dimer with inhibitor TL-3 bound and fragment 2F4 in the outside/top of flap
RCSB
Y
RCSB
2009-10-27
REL
REL
3TL
benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate
4DX
(1S,2S)-2-methylcyclohexanol
DMS
DIMETHYL SULFOXIDE
K
POTASSIUM ION
BME
BETA-MERCAPTOETHANOL
HOH
water
THE INHIBITOR IS A C2 SYMMETRIC HIV PROTEASE
2AZ8
HIV PR dimer generated from PDB entry 2AZ8
PDB
experimental model
Inhibitor
N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide
Peptide-like
3TL
200
2
3TL
3TL
200
A
4DX
201
3
4DX
4DX
201
A
DMS
303
4
DMS
DMS
303
A
DMS
304
4
DMS
DMS
304
A
DMS
305
4
DMS
DMS
305
A
K
307
5
K
K
307
A
BME
300
6
BME
BME
300
B
DMS
302
4
DMS
DMS
302
B
K
306
5
K
K
306
B
HOH
303
7
HOH
HOH
204
A
HOH
205
7
HOH
HOH
205
A
HOH
206
7
HOH
HOH
206
A
HOH
305
7
HOH
HOH
207
A
HOH
209
7
HOH
HOH
209
A
HOH
213
7
HOH
HOH
213
A
HOH
214
7
HOH
HOH
214
A
HOH
215
7
HOH
HOH
215
A
HOH
217
7
HOH
HOH
217
A
HOH
218
7
HOH
HOH
218
A
HOH
219
7
HOH
HOH
219
A
HOH
223
7
HOH
HOH
223
A
HOH
224
7
HOH
HOH
224
A
HOH
226
7
HOH
HOH
226
A
HOH
229
7
HOH
HOH
229
A
HOH
231
7
HOH
HOH
231
A
HOH
233
7
HOH
HOH
233
A
HOH
235
7
HOH
HOH
235
A
HOH
238
7
HOH
HOH
238
A
HOH
240
7
HOH
HOH
240
A
HOH
242
7
HOH
HOH
242
A
HOH
249
7
HOH
HOH
249
A
HOH
250
7
HOH
HOH
250
A
HOH
252
7
HOH
HOH
252
A
HOH
256
7
HOH
HOH
256
A
HOH
258
7
HOH
HOH
258
A
HOH
259
7
HOH
HOH
259
A
HOH
260
7
HOH
HOH
260
A
HOH
263
7
HOH
HOH
263
A
HOH
266
7
HOH
HOH
266
A
HOH
268
7
HOH
HOH
268
A
HOH
271
7
HOH
HOH
271
A
HOH
273
7
HOH
HOH
273
A
HOH
276
7
HOH
HOH
276
A
HOH
279
7
HOH
HOH
279
A
HOH
281
7
HOH
HOH
281
A
HOH
282
7
HOH
HOH
282
A
HOH
285
7
HOH
HOH
285
A
HOH
287
7
HOH
HOH
287
A
HOH
288
7
HOH
HOH
288
A
HOH
289
7
HOH
HOH
289
A
HOH
290
7
HOH
HOH
290
A
HOH
292
7
HOH
HOH
292
A
HOH
294
7
HOH
HOH
294
A
HOH
295
7
HOH
HOH
295
A
HOH
296
7
HOH
HOH
296
A
HOH
298
7
HOH
HOH
298
A
HOH
301
7
HOH
HOH
301
A
HOH
311
7
HOH
HOH
311
A
HOH
312
7
HOH
HOH
312
A
HOH
313
7
HOH
HOH
313
A
HOH
316
7
HOH
HOH
316
A
HOH
317
7
HOH
HOH
317
A
HOH
318
7
HOH
HOH
318
A
HOH
321
7
HOH
HOH
321
A
HOH
323
7
HOH
HOH
323
A
HOH
325
7
HOH
HOH
325
A
HOH
327
7
HOH
HOH
327
A
HOH
329
7
HOH
HOH
329
A
HOH
330
7
HOH
HOH
330
A
HOH
334
7
HOH
HOH
334
A
HOH
335
7
HOH
HOH
335
A
HOH
337
7
HOH
HOH
337
A
HOH
338
7
HOH
HOH
338
A
HOH
339
7
HOH
HOH
339
A
HOH
342
7
HOH
HOH
342
A
HOH
347
7
HOH
HOH
347
A
HOH
349
7
HOH
HOH
349
A
HOH
351
7
HOH
HOH
351
A
HOH
352
7
HOH
HOH
352
A
HOH
353
7
HOH
HOH
353
A
HOH
355
7
HOH
HOH
355
A
HOH
356
7
HOH
HOH
356
A
HOH
357
7
HOH
HOH
357
A
HOH
358
7
HOH
HOH
358
A
HOH
361
7
HOH
HOH
361
A
HOH
364
7
HOH
HOH
364
A
HOH
365
7
HOH
HOH
365
A
HOH
368
7
HOH
HOH
368
A
HOH
371
7
HOH
HOH
371
A
HOH
372
7
HOH
HOH
372
A
HOH
374
7
HOH
HOH
374
A
HOH
376
7
HOH
HOH
376
A
HOH
377
7
HOH
HOH
377
A
HOH
379
7
HOH
HOH
379
A
HOH
380
7
HOH
HOH
380
A
HOH
382
7
HOH
HOH
382
A
HOH
383
7
HOH
HOH
383
A
HOH
387
7
HOH
HOH
387
A
HOH
388
7
HOH
HOH
388
A
HOH
389
7
HOH
HOH
389
A
HOH
390
7
HOH
HOH
390
A
HOH
391
7
HOH
HOH
391
A
HOH
393
7
HOH
HOH
393
A
HOH
394
7
HOH
HOH
394
A
HOH
395
7
HOH
HOH
395
A
HOH
397
7
HOH
HOH
397
A
HOH
398
7
HOH
HOH
398
A
HOH
404
7
HOH
HOH
404
A
HOH
405
7
HOH
HOH
405
A
HOH
406
7
HOH
HOH
406
A
HOH
203
7
HOH
HOH
203
B
HOH
204
7
HOH
HOH
204
B
HOH
300
7
HOH
HOH
205
B
HOH
302
7
HOH
HOH
206
B
HOH
207
7
HOH
HOH
207
B
HOH
208
7
HOH
HOH
208
B
HOH
306
7
HOH
HOH
209
B
HOH
210
7
HOH
HOH
210
B
HOH
211
7
HOH
HOH
211
B
HOH
216
7
HOH
HOH
216
B
HOH
220
7
HOH
HOH
220
B
HOH
221
7
HOH
HOH
221
B
HOH
222
7
HOH
HOH
222
B
HOH
225
7
HOH
HOH
225
B
HOH
227
7
HOH
HOH
227
B
HOH
228
7
HOH
HOH
228
B
HOH
230
7
HOH
HOH
230
B
HOH
236
7
HOH
HOH
236
B
HOH
239
7
HOH
HOH
239
B
HOH
241
7
HOH
HOH
241
B
HOH
243
7
HOH
HOH
243
B
HOH
244
7
HOH
HOH
244
B
HOH
245
7
HOH
HOH
245
B
HOH
246
7
HOH
HOH
246
B
HOH
248
7
HOH
HOH
248
B
HOH
251
7
HOH
HOH
251
B
HOH
253
7
HOH
HOH
253
B
HOH
254
7
HOH
HOH
254
B
HOH
255
7
HOH
HOH
255
B
HOH
257
7
HOH
HOH
257
B
HOH
261
7
HOH
HOH
261
B
HOH
262
7
HOH
HOH
262
B
HOH
265
7
HOH
HOH
265
B
HOH
267
7
HOH
HOH
267
B
HOH
269
7
HOH
HOH
269
B
HOH
270
7
HOH
HOH
270
B
HOH
272
7
HOH
HOH
272
B
HOH
274
7
HOH
HOH
274
B
HOH
275
7
HOH
HOH
275
B
HOH
277
7
HOH
HOH
277
B
HOH
278
7
HOH
HOH
278
B
HOH
280
7
HOH
HOH
280
B
HOH
283
7
HOH
HOH
283
B
HOH
284
7
HOH
HOH
284
B
HOH
286
7
HOH
HOH
286
B
HOH
291
7
HOH
HOH
291
B
HOH
293
7
HOH
HOH
293
B
HOH
297
7
HOH
HOH
297
B
HOH
299
7
HOH
HOH
299
B
HOH
304
7
HOH
HOH
304
B
HOH
307
7
HOH
HOH
307
B
HOH
308
7
HOH
HOH
308
B
HOH
309
7
HOH
HOH
309
B
HOH
310
7
HOH
HOH
310
B
HOH
314
7
HOH
HOH
314
B
HOH
315
7
HOH
HOH
315
B
HOH
319
7
HOH
HOH
319
B
HOH
320
7
HOH
HOH
320
B
HOH
322
7
HOH
HOH
322
B
HOH
324
7
HOH
HOH
324
B
HOH
326
7
HOH
HOH
326
B
HOH
328
7
HOH
HOH
328
B
HOH
331
7
HOH
HOH
331
B
HOH
332
7
HOH
HOH
332
B
HOH
333
7
HOH
HOH
333
B
HOH
336
7
HOH
HOH
336
B
HOH
340
7
HOH
HOH
340
B
HOH
341
7
HOH
HOH
341
B
HOH
343
7
HOH
HOH
343
B
HOH
344
7
HOH
HOH
344
B
HOH
345
7
HOH
HOH
345
B
HOH
346
7
HOH
HOH
346
B
HOH
348
7
HOH
HOH
348
B
HOH
350
7
HOH
HOH
350
B
HOH
354
7
HOH
HOH
354
B
HOH
359
7
HOH
HOH
359
B
HOH
360
7
HOH
HOH
360
B
HOH
362
7
HOH
HOH
362
B
HOH
363
7
HOH
HOH
363
B
HOH
366
7
HOH
HOH
366
B
HOH
367
7
HOH
HOH
367
B
HOH
369
7
HOH
HOH
369
B
HOH
370
7
HOH
HOH
370
B
HOH
373
7
HOH
HOH
373
B
HOH
375
7
HOH
HOH
375
B
HOH
378
7
HOH
HOH
378
B
HOH
381
7
HOH
HOH
381
B
HOH
384
7
HOH
HOH
384
B
HOH
385
7
HOH
HOH
385
B
HOH
386
7
HOH
HOH
386
B
HOH
392
7
HOH
HOH
392
B
HOH
396
7
HOH
HOH
396
B
HOH
399
7
HOH
HOH
399
B
HOH
400
7
HOH
HOH
400
B
HOH
401
7
HOH
HOH
401
B
HOH
402
7
HOH
HOH
402
B
HOH
403
7
HOH
HOH
403
B
HOH
407
7
HOH
HOH
407
B
HOH
408
7
HOH
HOH
408
B
HOH
409
7
HOH
HOH
409
B
PRO
1
n
1
PRO
1
A
GLN
2
n
2
GLN
2
A
ILE
3
n
3
ILE
3
A
THR
4
n
4
THR
4
A
LEU
5
n
5
LEU
5
A
TRP
6
n
6
TRP
6
A
LYS
7
n
7
LYS
7
A
ARG
8
n
8
ARG
8
A
PRO
9
n
9
PRO
9
A
LEU
10
n
10
LEU
10
A
VAL
11
n
11
VAL
11
A
THR
12
n
12
THR
12
A
ILE
13
n
13
ILE
13
A
LYS
14
n
14
LYS
14
A
ILE
15
n
15
ILE
15
A
GLY
16
n
16
GLY
16
A
GLY
17
n
17
GLY
17
A
GLN
18
n
18
GLN
18
A
LEU
19
n
19
LEU
19
A
LYS
20
n
20
LYS
20
A
GLU
21
n
21
GLU
21
A
ALA
22
n
22
ALA
22
A
LEU
23
n
23
LEU
23
A
LEU
24
n
24
LEU
24
A
ASP
25
n
25
ASP
25
A
THR
26
n
26
THR
26
A
GLY
27
n
27
GLY
27
A
ALA
28
n
28
ALA
28
A
ASP
29
n
29
ASP
29
A
ASP
30
n
30
ASP
30
A
THR
31
n
31
THR
31
A
VAL
32
n
32
VAL
32
A
LEU
33
n
33
LEU
33
A
GLU
34
n
34
GLU
34
A
GLU
35
n
35
GLU
35
A
MET
36
n
36
MET
36
A
ASN
37
n
37
ASN
37
A
LEU
38
n
38
LEU
38
A
PRO
39
n
39
PRO
39
A
GLY
40
n
40
GLY
40
A
ARG
41
n
41
ARG
41
A
TRP
42
n
42
TRP
42
A
LYS
43
n
43
LYS
43
A
PRO
44
n
44
PRO
44
A
LYS
45
n
45
LYS
45
A
MET
46
n
46
MET
46
A
ILE
47
n
47
ILE
47
A
GLY
48
n
48
GLY
48
A
GLY
49
n
49
GLY
49
A
ILE
50
n
50
ILE
50
A
GLY
51
n
51
GLY
51
A
GLY
52
n
52
GLY
52
A
PHE
53
n
53
PHE
53
A
ILE
54
n
54
ILE
54
A
LYS
55
n
55
LYS
55
A
VAL
56
n
56
VAL
56
A
ARG
57
n
57
ARG
57
A
GLN
58
n
58
GLN
58
A
TYR
59
n
59
TYR
59
A
ASP
60
n
60
ASP
60
A
GLN
61
n
61
GLN
61
A
ILE
62
n
62
ILE
62
A
LEU
63
n
63
LEU
63
A
ILE
64
n
64
ILE
64
A
GLU
65
n
65
GLU
65
A
ILE
66
n
66
ILE
66
A
CYS
67
n
67
CYS
67
A
GLY
68
n
68
GLY
68
A
HIS
69
n
69
HIS
69
A
LYS
70
n
70
LYS
70
A
ALA
71
n
71
ALA
71
A
ILE
72
n
72
ILE
72
A
GLY
73
n
73
GLY
73
A
THR
74
n
74
THR
74
A
VAL
75
n
75
VAL
75
A
LEU
76
n
76
LEU
76
A
VAL
77
n
77
VAL
77
A
GLY
78
n
78
GLY
78
A
PRO
79
n
79
PRO
79
A
THR
80
n
80
THR
80
A
PRO
81
n
81
PRO
81
A
VAL
82
n
82
VAL
82
A
ASN
83
n
83
ASN
83
A
ILE
84
n
84
ILE
84
A
ILE
85
n
85
ILE
85
A
GLY
86
n
86
GLY
86
A
ARG
87
n
87
ARG
87
A
ASN
88
n
88
ASN
88
A
LEU
89
n
89
LEU
89
A
LEU
90
n
90
LEU
90
A
THR
91
n
91
THR
91
A
GLN
92
n
92
GLN
92
A
ILE
93
n
93
ILE
93
A
GLY
94
n
94
GLY
94
A
CYS
95
n
95
CYS
95
A
THR
96
n
96
THR
96
A
LEU
97
n
97
LEU
97
A
ASN
98
n
98
ASN
98
A
PHE
99
n
99
PHE
99
A
PRO
1
n
1
PRO
1
B
GLN
2
n
2
GLN
2
B
ILE
3
n
3
ILE
3
B
THR
4
n
4
THR
4
B
LEU
5
n
5
LEU
5
B
TRP
6
n
6
TRP
6
B
LYS
7
n
7
LYS
7
B
ARG
8
n
8
ARG
8
B
PRO
9
n
9
PRO
9
B
LEU
10
n
10
LEU
10
B
VAL
11
n
11
VAL
11
B
THR
12
n
12
THR
12
B
ILE
13
n
13
ILE
13
B
LYS
14
n
14
LYS
14
B
ILE
15
n
15
ILE
15
B
GLY
16
n
16
GLY
16
B
GLY
17
n
17
GLY
17
B
GLN
18
n
18
GLN
18
B
LEU
19
n
19
LEU
19
B
LYS
20
n
20
LYS
20
B
GLU
21
n
21
GLU
21
B
ALA
22
n
22
ALA
22
B
LEU
23
n
23
LEU
23
B
LEU
24
n
24
LEU
24
B
ASP
25
n
25
ASP
25
B
THR
26
n
26
THR
26
B
GLY
27
n
27
GLY
27
B
ALA
28
n
28
ALA
28
B
ASP
29
n
29
ASP
29
B
ASP
30
n
30
ASP
30
B
THR
31
n
31
THR
31
B
VAL
32
n
32
VAL
32
B
LEU
33
n
33
LEU
33
B
GLU
34
n
34
GLU
34
B
GLU
35
n
35
GLU
35
B
MET
36
n
36
MET
36
B
ASN
37
n
37
ASN
37
B
LEU
38
n
38
LEU
38
B
PRO
39
n
39
PRO
39
B
GLY
40
n
40
GLY
40
B
ARG
41
n
41
ARG
41
B
TRP
42
n
42
TRP
42
B
LYS
43
n
43
LYS
43
B
PRO
44
n
44
PRO
44
B
LYS
45
n
45
LYS
45
B
MET
46
n
46
MET
46
B
ILE
47
n
47
ILE
47
B
GLY
48
n
48
GLY
48
B
GLY
49
n
49
GLY
49
B
ILE
50
n
50
ILE
50
B
GLY
51
n
51
GLY
51
B
GLY
52
n
52
GLY
52
B
PHE
53
n
53
PHE
53
B
ILE
54
n
54
ILE
54
B
LYS
55
n
55
LYS
55
B
VAL
56
n
56
VAL
56
B
ARG
57
n
57
ARG
57
B
GLN
58
n
58
GLN
58
B
TYR
59
n
59
TYR
59
B
ASP
60
n
60
ASP
60
B
GLN
61
n
61
GLN
61
B
ILE
62
n
62
ILE
62
B
LEU
63
n
63
LEU
63
B
ILE
64
n
64
ILE
64
B
GLU
65
n
65
GLU
65
B
ILE
66
n
66
ILE
66
B
CYS
67
n
67
CYS
67
B
GLY
68
n
68
GLY
68
B
HIS
69
n
69
HIS
69
B
LYS
70
n
70
LYS
70
B
ALA
71
n
71
ALA
71
B
ILE
72
n
72
ILE
72
B
GLY
73
n
73
GLY
73
B
THR
74
n
74
THR
74
B
VAL
75
n
75
VAL
75
B
LEU
76
n
76
LEU
76
B
VAL
77
n
77
VAL
77
B
GLY
78
n
78
GLY
78
B
PRO
79
n
79
PRO
79
B
THR
80
n
80
THR
80
B
PRO
81
n
81
PRO
81
B
VAL
82
n
82
VAL
82
B
ASN
83
n
83
ASN
83
B
ILE
84
n
84
ILE
84
B
ILE
85
n
85
ILE
85
B
GLY
86
n
86
GLY
86
B
ARG
87
n
87
ARG
87
B
ASN
88
n
88
ASN
88
B
LEU
89
n
89
LEU
89
B
LEU
90
n
90
LEU
90
B
THR
91
n
91
THR
91
B
GLN
92
n
92
GLN
92
B
ILE
93
n
93
ILE
93
B
GLY
94
n
94
GLY
94
B
CYS
95
n
95
CYS
95
B
THR
96
n
96
THR
96
B
LEU
97
n
97
LEU
97
B
ASN
98
n
98
ASN
98
B
PHE
99
n
99
PHE
99
B
author_and_software_defined_assembly
PISA
2
dimeric
3510
-23
10000
A
GLY
94
A
O
GLY
94
1_555
A
K
307
H
K
K
1_555
A
THR
96
A
OG1
THR
96
1_555
102.2
A
GLY
94
A
O
GLY
94
1_555
A
K
307
H
K
K
1_555
A
HOH
355
L
O
HOH
1_555
64.9
A
THR
96
A
OG1
THR
96
1_555
A
K
307
H
K
K
1_555
A
HOH
355
L
O
HOH
1_555
162.9
A
GLY
94
A
O
GLY
94
1_555
A
K
307
H
K
K
1_555
B
ASN
98
B
O
ASN
98
1_555
72.3
A
THR
96
A
OG1
THR
96
1_555
A
K
307
H
K
K
1_555
B
ASN
98
B
O
ASN
98
1_555
77.5
A
HOH
355
L
O
HOH
1_555
A
K
307
H
K
K
1_555
B
ASN
98
B
O
ASN
98
1_555
107.2
A
GLY
94
A
O
GLY
94
1_555
A
K
307
H
K
K
1_555
B
HOH
239
M
O
HOH
1_555
85.4
A
THR
96
A
OG1
THR
96
1_555
A
K
307
H
K
K
1_555
B
HOH
239
M
O
HOH
1_555
92.4
A
HOH
355
L
O
HOH
1_555
A
K
307
H
K
K
1_555
B
HOH
239
M
O
HOH
1_555
75.9
B
ASN
98
B
O
ASN
98
1_555
A
K
307
H
K
K
1_555
B
HOH
239
M
O
HOH
1_555
152.7
A
GLY
94
A
O
GLY
94
1_555
A
K
307
H
K
K
1_555
B
HOH
384
M
O
HOH
1_555
166.5
A
THR
96
A
OG1
THR
96
1_555
A
K
307
H
K
K
1_555
B
HOH
384
M
O
HOH
1_555
90.1
A
HOH
355
L
O
HOH
1_555
A
K
307
H
K
K
1_555
B
HOH
384
M
O
HOH
1_555
101.9
B
ASN
98
B
O
ASN
98
1_555
A
K
307
H
K
K
1_555
B
HOH
384
M
O
HOH
1_555
116.6
B
HOH
239
M
O
HOH
1_555
A
K
307
H
K
K
1_555
B
HOH
384
M
O
HOH
1_555
88.4
A
ASN
98
A
O
ASN
98
1_555
B
K
306
K
K
K
1_555
B
GLY
94
B
O
GLY
94
1_555
78.3
A
ASN
98
A
O
ASN
98
1_555
B
K
306
K
K
K
1_555
B
THR
96
B
OG1
THR
96
1_555
75.2
B
GLY
94
B
O
GLY
94
1_555
B
K
306
K
K
K
1_555
B
THR
96
B
OG1
THR
96
1_555
110.8
A
ASN
98
A
O
ASN
98
1_555
B
K
306
K
K
K
1_555
B
HOH
354
M
O
HOH
1_555
146.9
B
GLY
94
B
O
GLY
94
1_555
B
K
306
K
K
K
1_555
B
HOH
354
M
O
HOH
1_555
69.5
B
THR
96
B
OG1
THR
96
1_555
B
K
306
K
K
K
1_555
B
HOH
354
M
O
HOH
1_555
108.7
A
ASN
98
A
O
ASN
98
1_555
B
K
306
K
K
K
1_555
B
HOH
399
M
O
HOH
1_555
116.0
B
GLY
94
B
O
GLY
94
1_555
B
K
306
K
K
K
1_555
B
HOH
399
M
O
HOH
1_555
66.4
B
THR
96
B
OG1
THR
96
1_555
B
K
306
K
K
K
1_555
B
HOH
399
M
O
HOH
1_555
166.5
B
HOH
354
M
O
HOH
1_555
B
K
306
K
K
K
1_555
B
HOH
399
M
O
HOH
1_555
57.8
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
ILE
3
A
N
ILE
3
B
O
LEU
97
B
O
LEU
97
B
O
THR
96
B
O
THR
96
A
N
ASN
98
A
N
ASN
98
A
N
LEU
97
A
N
LEU
97
B
O
ILE
3
B
O
ILE
3
A
N
LYS
45
A
N
LYS
45
A
O
VAL
56
A
O
VAL
56
A
N
ARG
57
A
N
ARG
57
A
O
VAL
77
A
O
VAL
77
A
O
LEU
76
A
O
LEU
76
A
N
LEU
33
A
N
LEU
33
A
N
VAL
32
A
N
VAL
32
A
O
ILE
84
A
O
ILE
84
A
O
ILE
85
A
O
ILE
85
A
N
LEU
23
A
N
LEU
23
A
O
ALA
22
A
O
ALA
22
A
N
VAL
11
A
N
VAL
11
A
N
LYS
14
A
N
LYS
14
A
O
GLU
65
A
O
GLU
65
B
N
LYS
43
B
N
LYS
43
B
O
GLN
58
B
O
GLN
58
B
N
ARG
57
B
N
ARG
57
B
O
VAL
77
B
O
VAL
77
B
O
LEU
76
B
O
LEU
76
B
N
LEU
33
B
N
LEU
33
B
N
VAL
32
B
N
VAL
32
B
O
ILE
84
B
O
ILE
84
B
O
ILE
85
B
O
ILE
85
B
N
LEU
23
B
N
LEU
23
B
O
LYS
20
B
O
LYS
20
B
N
ILE
13
B
N
ILE
13
B
N
LYS
14
B
N
LYS
14
B
O
GLU
65
B
O
GLU
65
1
A
C18
3TL
200
PLANAR
A
1
A
C18
3TL
200
PLANAR
B
1
A
C2
3TL
200
PLANAR
A
1
A
C2
3TL
200
PLANAR
B
1
A
C68
3TL
200
PLANAR
A
1
A
C68
3TL
200
PLANAR
B
1
A
A
O
O
ALA
HOH
28
361
1.72
1
A
A
OD2
O1
ASP
3TL
25
200
2.17
A
1
A
GLU
35
-37.37
125.68
76.23
32.903
18.14
3.680
0.000
0.000
-1.940
0.000
-1.730
0.953
0.928
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
0.274
0.214
0.217
1.770
48.550
1136
23368
21866
5.200
92.580
1.00
0.50
3.905
0.122
RANDOM
1
THROUGHOUT
0.00
MOLECULAR REPLACEMENT
0.149
0.153
0.800
0.800
1.400
HIV PR dimer generated from PDB entry 2AZ8
MAXIMUM LIKELIHOOD
MASK
1.770
48.550
201
1815
96
0
1518
0.023
0.021
1904
1.884
2.027
2899
6.461
7.500
392
42.718
24.815
54
14.318
15.000
288
20.329
15.000
8
0.145
0.200
262
0.007
0.021
2048
1.346
1.500
979
2.217
2.000
1592
3.357
3.000
729
4.955
4.500
709
0.367
0.340
1.816
79
1489
1568
1489
20
91.220
27.9
1.770
48.564
3KFN
23368
21896
0.0
0.0
0.089
0.089
1
3.0
3.4
93.7
0.637
1.77
1.82
1.1
1574
0.637
1
3.4
92.5
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
5.5.0072
data extraction
PDB
help@deposit.rcsb.org
June 11, 2008
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.005
data collection
Blu-Ice
data reduction
MOSFLM
data scaling
SCALA
phasing
MOLREP
HIV Protease (PR) with inhibitor TL-3 and fragment hit 4D9 by soaking
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
4
N
N
5
N
N
6
N
N
4
N
N
5
N
N
7
N
N
7
N
N
A
GLY
86
A
GLY
86
HELX_P
A
THR
91
A
THR
91
1
1
6
B
GLY
86
B
GLY
86
HELX_P
B
GLY
94
B
GLY
94
1
2
9
metalc
2.882
A
GLY
94
A
O
GLY
94
1_555
A
K
307
H
K
K
1_555
metalc
2.972
A
THR
96
A
OG1
THR
96
1_555
A
K
307
H
K
K
1_555
metalc
2.734
A
ASN
98
A
O
ASN
98
1_555
B
K
306
K
K
K
1_555
metalc
2.910
A
K
307
H
K
K
1_555
A
HOH
355
L
O
HOH
1_555
metalc
2.972
A
K
307
H
K
K
1_555
B
ASN
98
B
O
ASN
98
1_555
metalc
3.496
A
K
307
H
K
K
1_555
B
HOH
239
M
O
HOH
1_555
metalc
3.319
A
K
307
H
K
K
1_555
B
HOH
384
M
O
HOH
1_555
metalc
2.684
B
GLY
94
B
O
GLY
94
1_555
B
K
306
K
K
K
1_555
metalc
3.057
B
THR
96
B
OG1
THR
96
1_555
B
K
306
K
K
K
1_555
metalc
2.826
B
K
306
K
K
K
1_555
B
HOH
354
M
O
HOH
1_555
metalc
2.987
B
K
306
K
K
K
1_555
B
HOH
399
M
O
HOH
1_555
HYDROLASE/HYDROLASE INHIBITOR
HIV-1, PROTEASE, EXO SITE, Aspartyl protease, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Q903N5_9HIV1
UNP
1
1
Q903N5
PQITLWRRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
1
99
3KFN
1
99
Q903N5
A
1
1
99
1
99
3KFN
1
99
Q903N5
B
1
1
99
1
ARG
engineered mutation
LYS
7
3KFN
A
Q903N5
UNP
7
7
2
ARG
engineered mutation
LYS
7
3KFN
B
Q903N5
UNP
7
7
4
8
8
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
GLN
2
A
GLN
2
A
ILE
3
A
ILE
3
B
THR
96
B
THR
96
B
ASN
98
B
ASN
98
A
THR
96
A
THR
96
A
ASN
98
A
ASN
98
B
GLN
2
B
GLN
2
B
ILE
3
B
ILE
3
A
LYS
43
A
LYS
43
A
GLY
49
A
GLY
49
A
GLY
52
A
GLY
52
A
ILE
66
A
ILE
66
A
HIS
69
A
HIS
69
A
VAL
77
A
VAL
77
A
VAL
32
A
VAL
32
A
LEU
33
A
LEU
33
A
ILE
84
A
ILE
84
A
ILE
85
A
ILE
85
A
GLN
18
A
GLN
18
A
LEU
24
A
LEU
24
A
LEU
10
A
LEU
10
A
ILE
15
A
ILE
15
A
GLY
52
A
GLY
52
A
ILE
66
A
ILE
66
B
LYS
43
B
LYS
43
B
GLY
49
B
GLY
49
B
GLY
52
B
GLY
52
B
ILE
66
B
ILE
66
B
HIS
69
B
HIS
69
B
VAL
77
B
VAL
77
B
VAL
32
B
VAL
32
B
LEU
33
B
LEU
33
B
ILE
84
B
ILE
84
B
ILE
85
B
ILE
85
B
GLN
18
B
GLN
18
B
LEU
24
B
LEU
24
B
LEU
10
B
LEU
10
B
ILE
15
B
ILE
15
B
GLY
52
B
GLY
52
B
ILE
66
B
ILE
66
BINDING SITE FOR RESIDUE 3TL A 200
A
3TL
200
Software
34
BINDING SITE FOR RESIDUE 4DX A 201
A
4DX
201
Software
8
BINDING SITE FOR RESIDUE DMS A 303
A
DMS
303
Software
9
BINDING SITE FOR RESIDUE DMS A 304
A
DMS
304
Software
4
BINDING SITE FOR RESIDUE DMS A 305
A
DMS
305
Software
6
BINDING SITE FOR RESIDUE K A 307
A
K
307
Software
4
BINDING SITE FOR RESIDUE BME B 300
B
BME
300
Software
6
BINDING SITE FOR RESIDUE DMS B 302
B
DMS
302
Software
7
BINDING SITE FOR RESIDUE K B 306
B
K
306
Software
5
A
TRP
6
A
TRP
6
34
4_456
A
ARG
8
A
ARG
8
34
1_555
A
ASP
25
A
ASP
25
34
1_555
A
GLY
27
A
GLY
27
34
1_555
A
ALA
28
A
ALA
28
34
1_555
A
ASP
29
A
ASP
29
34
1_555
A
ASP
30
A
ASP
30
34
1_555
A
LYS
45
A
LYS
45
34
1_555
A
MET
46
A
MET
46
34
1_555
A
ILE
47
A
ILE
47
34
1_555
A
GLY
48
A
GLY
48
34
1_555
A
GLY
49
A
GLY
49
34
1_555
A
ILE
50
A
ILE
50
34
1_555
A
PHE
53
A
PHE
53
34
1_555
A
PRO
81
A
PRO
81
34
1_555
A
VAL
82
A
VAL
82
34
1_555
A
ILE
84
A
ILE
84
34
1_555
A
DMS
303
E
DMS
34
1_555
A
HOH
358
L
HOH
34
1_555
A
HOH
364
L
HOH
34
1_555
B
ARG
8
B
ARG
8
34
1_555
B
LEU
23
B
LEU
23
34
1_555
B
ASP
25
B
ASP
25
34
1_555
B
GLY
27
B
GLY
27
34
1_555
B
ALA
28
B
ALA
28
34
1_555
B
ASP
29
B
ASP
29
34
1_555
B
GLY
48
B
GLY
48
34
1_555
B
GLY
49
B
GLY
49
34
1_555
B
ILE
50
B
ILE
50
34
1_555
B
PHE
53
B
PHE
53
34
1_555
B
PRO
81
B
PRO
81
34
1_555
B
VAL
82
B
VAL
82
34
1_555
B
ILE
84
B
ILE
84
34
1_555
B
HOH
203
M
HOH
34
1_555
A
LYS
14
A
LYS
14
8
1_555
A
ILE
15
A
ILE
15
8
1_555
A
GLY
16
A
GLY
16
8
1_555
A
GLY
17
A
GLY
17
8
1_555
A
LEU
63
A
LEU
63
8
1_555
A
ILE
64
A
ILE
64
8
1_555
A
GLU
65
A
GLU
65
8
1_555
A
HOH
301
L
HOH
8
1_555
A
TRP
6
A
TRP
6
9
4_456
A
GLY
49
A
GLY
49
9
1_555
A
ILE
50
A
ILE
50
9
1_555
A
GLY
51
A
GLY
51
9
1_555
A
GLY
52
A
GLY
52
9
1_555
A
3TL
200
C
3TL
9
1_555
B
ILE
54
B
ILE
54
9
1_555
B
PRO
79
B
PRO
79
9
1_555
B
PRO
81
B
PRO
81
9
1_555
A
GLY
73
A
GLY
73
4
1_555
A
THR
74
A
THR
74
4
1_555
A
ASN
88
A
ASN
88
4
1_555
B
ARG
41
B
ARG
41
4
3_546
A
ARG
87
A
ARG
87
6
1_555
A
ASN
88
A
ASN
88
6
1_555
A
THR
91
A
THR
91
6
1_555
B
LEU
5
B
LEU
5
6
1_555
B
TRP
6
B
TRP
6
6
1_555
B
ARG
41
B
ARG
41
6
3_546
A
GLY
94
A
GLY
94
4
1_555
A
THR
96
A
THR
96
4
1_555
A
HOH
355
L
HOH
4
1_555
B
ASN
98
B
ASN
98
4
1_555
A
GLN
18
A
GLN
18
6
1_556
A
ASN
37
A
ASN
37
6
1_556
B
THR
12
B
THR
12
6
1_555
B
GLU
65
B
GLU
65
6
1_555
B
CYS
67
B
CYS
67
6
1_555
B
GLY
68
B
GLY
68
6
1_555
B
LYS
14
B
LYS
14
7
1_555
B
GLY
16
B
GLY
16
7
1_555
B
GLY
17
B
GLY
17
7
1_555
B
LEU
63
B
LEU
63
7
1_555
B
ILE
64
B
ILE
64
7
1_555
B
GLU
65
B
GLU
65
7
1_555
B
LYS
70
B
LYS
70
7
1_555
A
ASN
98
A
ASN
98
5
1_555
B
GLY
94
B
GLY
94
5
1_555
B
THR
96
B
THR
96
5
1_555
B
HOH
354
M
HOH
5
1_555
B
HOH
399
M
HOH
5
1_555
18
P 21 21 2